/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2020 UniPro <ugene@unipro.ru>
 * http://ugene.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301, USA.
 */

#ifndef _U2_VECTOR_NTI_SEQUENCE_FORMAT_H_
#define _U2_VECTOR_NTI_SEQUENCE_FORMAT_H_

#include <U2Core/AnnotationData.h>

#include "GenbankPlainTextFormat.h"

namespace U2 {

class AnnotationGroup;

class U2FORMATS_EXPORT VectorNtiSequenceFormat : public GenbankPlainTextFormat {
    Q_OBJECT
public:
    VectorNtiSequenceFormat(QObject *parent);

    virtual void storeEntry(IOAdapter *io, const QMap<GObjectType, QList<GObject *>> &objectsMap, U2OpStatus &os);

private:
    virtual FormatCheckResult checkRawTextData(const QByteArray &rawData, const GUrl & = GUrl()) const;

    QList<StrPair> processCommentKeys(QMultiMap<QString, QVariant> &tags);
    void createCommentAnnotation(const QStringList &comments, int sequenceLength, AnnotationTableObject *annTable) const;
    U2Qualifier createQualifier(const QString &qualifierName, const QString &qualifierValue, bool containsDoubleQuotes) const;
    U2FeatureType getFeatureType(const QString &typeString) const;
    QString getFeatureTypeString(U2FeatureType featureType, bool isAmino) const;
    StrStrMap parseComments(const QStringList &comments) const;
    static QString parseDate(int date);
    QList<SharedAnnotationData> prepareAnnotations(const QList<GObject *> &tablesList, bool isAmino, U2OpStatus &os) const;
    void writeAnnotations(IOAdapter *io, const QList<GObject *> &aos, bool isAmino, U2OpStatus &os);
    void prepareQualifiersToWrite(QMap<AnnotationGroup *, QList<SharedAnnotationData>> &annotationsByGroups, bool isAmino) const;

    enum VntiDnaFeatureTypes {
        DnaAttenuator = 0,
        DnaBHlhDomain = 1,
        DnaCRegion = 2,
        DnaCaatSignal = 3,
        DnaCds = 4,
        DnaCentromere = 5,
        DnaDLoop = 6,
        DnaDSegment = 7,
        DnaEnhancer = 9,
        DnaGcSignal = 10,
        DnaGlycosylationSite = 11,
        DnaHomeodomain = 12,
        DnaIDna = 13,
        DnaInsertion = 14,
        DnaIntron = 15,
        DnaJSegment = 16,
        DnaLeucineZipperDomain = 17,
        DnaLoci = 18,
        DnaLtr = 19,
        DnaMiscBindingSite = 20,
        DnaMiscFeature = 21,
        DnaMiscMarker = 22,
        DnaModifiedBase = 23,
        DnaNRegion = 24,
        DnaPolyASignal = 25,
        DnaPolyASite = 26,
        DnaPrimer = 27,
        DnaPrimerBindingSite = 28,
        DnaPromoterEukaryotic = 29,
        DnaPromoterProkaryotic = 30,
        DnaProteinBindingSite = 31,
        DnaRbs = 32,
        DnaReplicationOrigin = 33,
        DnaRepeatRegion = 34,
        DnaRepeatUnit = 35,
        DnaSRegion = 36,
        DnaSilencer = 37,
        DnaSplicingSignal = 38,
        DnaStemLoop = 39,
        DnaSts = 40,
        DnaTataSignal = 41,
        DnaTelomere = 42,
        DnaTerminator = 43,
        DnaTransposon = 44,
        DnaVRegion = 45,
        DnaZincFingerDomain = 46,
        DnaMinus10Signal = 47,
        DnaMinus35Signal = 48,
        DnaThreePrimeClip = 49,
        DnaThreePrimeUtr = 50,
        DnaFivePrimeClip = 51,
        DnaFivePrimeUtr = 52,
        DnaRnaMisc = 53,
        DnaMRna = 54,
        DnaPrecursorRna = 55,
        DnaScRna = 56,
        DnaSnRna = 57,
        DnaRRna = 58,
        DnaTRna = 59,
        DnaGene = 60,
        DnaExon = 61,
        DnaMutation = 62,
        DnaAllele = 81,
        DnaCellular = 82,
        DnaConflict = 83,
        DnaMaturePeptide = 84,
        DnaMiscDifference = 85,
        DnaMiscRecombination = 86,
        DnaMiscSignal = 87,
        DnaMiscStructure = 88,
        DnaOldSequence = 89,
        DnaPrimerTranscript = 91,
        DnaProvirus = 92,
        DnaSatellite = 93,
        DnaSignalPeptide = 94,
        DnaTransitPeptide = 95,
        DnaVariation = 96,
        DnaVirion = 97,
        DnaSource = 98,
        DnaUnsure = 99,
        DnaVSegment = 100,
        DnaGap = 102,
        DnaOperon = 103,
        DnaOriT = 104,
        DnaSnoRna = 105,
        DnaOverhang = 274
    };

    enum VntiProteinFeatureTypes {
        ProteinSignalSequence = 200,
        ProteinTransitPeptide = 201,
        ProteinPropeptide = 202,
        ProteinMatureChain = 203,
        ProteinProcessedActivePeptide = 204,
        ProteinRepetitiveRegion = 205,
        ProteinSimilarity = 206,
        ProteinHelicalRegion = 207,
        ProteinHydrogenBondedTurn = 208,
        ProteinBetaStrandRegion = 209,
        ProteinTransmembraneRegion = 210,
        ProteinCalcium = 211,
        ProteinDnaRnaBindingRegionMisc = 212,
        ProteinNpBindingRegionMisc = 213,
        ProteinCellAttachment = 219,
        ProteinActiveSite = 220,
        ProteinCleavageSite = 221,
        ProteinHemeBindingSite = 223,
        ProteinPyridoxalPhBindingSite = 224,
        ProteinBiotinBindingSite = 225,
        ProteinCholesterolBindingSite = 226,
        ProteinAcetylation = 227,
        ProteinAdenylation = 228,
        ProteinAmidation = 229,
        ProteinBlocked = 230,
        ProteinFormylation = 231,
        ProteinGammaCarboxyglumaticAcid = 232,
        ProteinHydroxylation = 233,
        ProteinMethylation = 234,
        ProteinPhosphorylation = 235,
        ProteinPyrrolidoneCarboxylicAcid = 236,
        ProteinSulfatation = 237,
        ProteinGlycosylation = 238,
        ProteinResidueModificationMisc = 239,
        ProteinConflict = 240,
        ProteinVariant = 241,
        ProteinSplicingVariant = 242,
        ProteinAlteredSite = 243,
        ProteinNonConsecutiveResidues = 244,
        ProteinUncertainty = 245,
        ProteinMyristate = 248,
        ProteinPalmitate = 249,
        ProteinFarnesyl = 250,
        ProteinGeranylGeranyl = 251,
        ProteinGpiAnchor = 252,
        ProteinNAcylDiglyceride = 253,
        ProteinDisulfide = 254,
        ProteinThiolester = 255,
        ProteinThioether = 256,
        ProteinLipidMisc = 262,
        ProteinBondMisc = 263,
        ProteinMetalMisc = 264,
        ProteinSiteMisc = 265,
        ProteinRegionMisc = 266,
        ProteinSource = 269,
        ProteinProprotein = 272,
        ProteinMiscFeature = 273,
        ProteinVariation = 275,
        ProteinPrecursor = 276,
        ProteinSeconadaryStructure = 277,
        ProteinDomainMisc = 1000,
        ProteinExtracellular = 1001,
        ProteinIntracellular = 1002,
        ProteinConnectingPeptide = 1003,
        ProteinCytoplasmic = 1004,
        ProteinPeriplasmic = 1005,
        ProteinExoplasmic = 1006,
        ProteinBindingSiteMisc = 1007,
        ProteinCatalyticRegion = 1008,
        ProteinKinase = 1011,
        ProteinProtease = 1012,
        ProteinNuclease = 1013,
        ProteinAaRich = 1014,
        ProteinPolyAa = 1015,
        ProteinCub = 1016,
        ProteinEgf = 1017,
        ProteinFibronectin = 1018,
        ProteinImmunoglobulin = 1019,
        ProteinLeucineZipper = 1020,
        ProteinC2 = 1021,
        ProteinCoiledCoil = 1022,
        ProteinKh = 1024,
        ProteinPh = 1025,
        ProteinSh2 = 1026,
        ProteinSh3 = 1027,
        ProteinZincFinger = 1028,
        ProteinCollagenType = 1029,
        ProteinBasic = 1030,
        ProteinHmgBox = 1031,
        ProteinHomeodomain = 1032,
        ProteinHth = 1033,
        ProteinAlphaHelix = 1100,
        ProteinBetaSheet = 1101
    };

    static const QString vntiCreationDateKey;
    static const QString vntiModificationDateKey;
    static const StrStrMap vntiMetaKeys;    // keys in the comment section
    static const QMap<U2FeatureType, VntiDnaFeatureTypes> dnaFeatureTypesMap;    // UGENE feature type - vntifkey qualifier value for DNA sequences
    static const QMap<U2FeatureType, VntiProteinFeatureTypes> proteinFeatureTypesMap;    // UGENE feature type - vntifkey qualifier value for protein sequences
    static const QMap<VntiDnaFeatureTypes, QString> dnaFeatureType2StringMap;    // vntifkey qualifier value - feature type name in vnti file for DNA files
    static const QMap<VntiProteinFeatureTypes, QString> proteinFeatureType2StringMap;    // vntifkey qualifier value - feature type name in vnti file for protein files
    static const QString DEFAULT_FEATURE_TYPE_NAME;
    static const QString QUALIFIER_LABEL;
    static const QString VNTIFKEY_QUALIFIER_NAME;

    static StrStrMap initVntiMetaKeys();
    static QMap<U2FeatureType, VntiDnaFeatureTypes> initDnaFeatureTypesMap();
    static QMap<U2FeatureType, VntiProteinFeatureTypes> initProteinFeatureTypesMap();
    static QMap<VntiDnaFeatureTypes, QString> initDnaFeatureType2StringMap();
    static QMap<VntiProteinFeatureTypes, QString> initProteinFeatureType2StringMap();
};

}    // namespace U2

#endif    // _U2_VECTOR_NTI_SEQUENCE_FORMAT_H_
